CODECHECK certificate 2024-019

Summary

This codecheck was done as part of the “CodeCheck goes NL” workshop in Erasmus University Rotterdam, The Netherlands. The codechek process was carried out in two stages. During the workshop, the reproduction of Figure 5 in the manuscript was achieved with help from the authors. Following the workshop, the authors provided the codecheckers with a Jupyter notebook capable of generating most of the figures presented in the manuscript, along with those in the supplementary materials.

CODECHECKER notes

The authors have made available the necessary code and data to reproduce the figures and tables in the manuscript and supplementary documentation. These resources can be accessed at https://osf.io/y2q3r/.

Reproduction of Figure 5

Figure 5 was reproduced by running the Jupyter notebook Empatica.ipynb(https://osf.io/7h48c). The authors assisted the codecheckers in fixing minor issues in the code, mainly related to incorrect paths to the data files needed to generate the plot. The following changes were made to the code:

• Modified the path variable in the notebook’s second cell; its value was set to <local-path>/osfstorage-archive/Raw Data/Empatica Avro Files
• Modified the events_path variable the fourth cell; its value was set to <local-path>/osfstorage-archive/Raw Data/" + pp + "_events.csv

All the necessary libraries to run the notebooks, except for Jupyter itself, were obtained by installing the wearablehrv package as documented in the README file of the repository https://github.com/Aminsinichi/wearable-hrv.

Reproduction of all other figures and tables

Following the workshop, the authors uploaded to the article’s OSF project the Jupyter notebook Quality in Question - Reproduce Results.ipynb (https://osf.io/x6t5n) which was used by the codecheckers to reproduce all the other figures and tables included in this report.

Recommendations

The codechekers suggest to the authors to consider the following suggestions for their next publication or workflow:

• Providing readers with jupyter notebooks that generate all the figures in the article. These notebooks can be submitted along with the article, as supplementary documentation.
• Using the function os.path.join to handle the paths in Python code

Manifest files

fig2_empatica.png

Comment: manuscript Fig. 2 (empatica)

fig2_heartmath.png

Comment: manuscript Fig. 2 (heartmath)

fig2_kyto.png

Comment: manuscript Fig. 2 (kyto)

fig2_rhythm.png

Comment: manuscript Fig. 2 (rhythm)

fig4_meanhr.png

Comment: manuscript Fig. 4 (mean hr)

fig4_rmssd.png

Comment: manuscript Fig. 4 (rmssd)

fig5.png

Comment: manuscript Fig. 5

fig6_arithmetic_meanhr.png

Comment: manuscript Fig. 6 (arithmetic, meanhr)

fig6_arithmetic_rmssd.png

Comment: manuscript Fig. 6 (arithmetic, rmssd)

fig6_biking_meanhr.png

Comment: manuscript Fig. 6 (biking, mean hr)

fig6_biking_rmssd.png

Comment: manuscript Fig. 6 (biking, rmssd)

fig6_sitting_meanhr.png

Comment: manuscript Fig. 6 (sitting, mean hr)

fig6_sitting_rmssd.png

Comment: manuscript Fig. 6 (sitting, rmssd)

fig7_meanhr.png

Comment: manuscript Fig. 7 (mean hr)

fig7_rmssd.png

Comment: manuscript Fig. 7 (rmssd)

fig8_meanhr.png

Comment: manuscript Fig. 8 (mean hr)

fig8_rmssd.png

Comment: manuscript Fig. 8 (rmssd)

fig9_arithmetic_meanhr.png

Comment: manuscript Fig. 9 (arithmetic, meanhr)

fig9_arithmetic_rmssd.png

Comment: manuscript Fig. 9 (arithmetic, rmssd)

fig9_biking_meanhr.png

Comment: manuscript Fig. 9 (biking, mean hr)

fig9_biking_rmssd.png

Comment: manuscript Fig. 9 (biking, rmssd)

fig9_sitting_meanhr.png

Comment: manuscript Fig. 9 (sitting, mean hr)

fig9_sitting_rmssd.png

Comment: manuscript Fig. 9 (sitting, rmssd)

table1.png

Comment: manuscript Table 1

sfig4_empatica.png

Comment: supplement Fig. 4 (empatica)

sfig4_heartmath.png

Comment: supplement Fig. 4 (heartmath)

sfig4_kyto.png

Comment: supplement Fig. 4 (kyto)

sfig4_rhythm.png

Comment: supplement Fig. 4 (rhythm)

sfig5_empatica.png

Comment: supplement Fig. 5 (empatica)

sfig5_heartmath.png

Comment: supplement Fig. 5 (heartmath)

sfig5_kyto.png

Comment: supplement Fig. 5 (kyto)

sfig5_rhythm.png

Comment: supplement Fig. 5 (rhythm)

sfig6_empatica.png

Comment: supplement Fig. 6 (empatica)

sfig6_heartmath.png

Comment: supplement Fig. 6 (heartmath)

sfig6_kyto.png

Comment: supplement Fig. 6 (kyto)

sfig6_rhythm.png

Comment: supplement Fig. 6 (rhythm)

sfig7_kyto.png

Comment: supplement Fig. 7 (kyto)

sfig7_rhythm.png

Comment: supplement Fig. 7 (rhythm)

sfig8_empatica.png

Comment: supplement Fig. 8 (empatica)

sfig8_heartmath.png

Comment: supplement Fig. 8 (heartmath)

sfig9_kyto.png

Comment: supplement Fig. 9 (kyto)

sfig9_rhythm.png

Comment: supplement Fig. 9 (rhythm)

stable3.png

Comment: supplement Table 3

stable4.png

Comment: supplement Table 4

stable5.png

Comment: supplement Table 5

Acknowledgements

We would like to acknowledge NWO for funding the CHECK-NL project, and enabling the workshop at Rotterdam.

Citing this document

Yasel Quintero, Tornike Skhirtladze, Joslyn Sun, Gabriella Low Chew Tung, Roel Janssen (2024). CODECHECK Certificate 2024-019. Zenodo. https://doi.org/10.5281/zenodo.FIXME

About CODECHECK

This certificate confirms that the codecheckers could independently reproduce the results of a computational analysis given the data and code from a third party. A CODECHECK does not check whether the original computation analysis is correct. However, as all materials required for the reproduction are freely available by following the links in this document, the reader can then study for themselves the code and data.

About this document

This document was created using R Markdown using the codecheck R package. make codecheck.pdf will regenerate the report file.

sessionInfo()

## R version 4.4.1 (2024-06-14)
## Platform: aarch64-apple-darwin20
## Running under: macOS 15.1.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
## 
## locale:
## [1] C/UTF-8/C/C/C/C
## 
## time zone: Europe/Amsterdam
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets 
## [6] methods   base     
## 
## other attached packages:
##  [1] readr_2.1.5      tibble_3.2.1     xtable_1.8-4    
##  [4] yaml_2.3.10      rprojroot_2.0.4  knitr_1.49      
##  [7] codecheck_0.11.4 parsedate_1.3.1  R.cache_0.16.0  
## [10] gh_1.4.1        
## 
## loaded via a namespace (and not attached):
##  [1] xfun_0.49         bslib_0.8.0       rdflib_0.2.9     
##  [4] tzdb_0.4.0        vctrs_0.6.5       tools_4.4.1      
##  [7] generics_0.1.3    parallel_4.4.1    curl_6.0.1       
## [10] fansi_1.0.6       pkgconfig_2.0.3   pdftools_3.4.1   
## [13] R.oo_1.27.0       redland_1.0.17-18 assertthat_0.2.1 
## [16] lifecycle_1.0.4   compiler_4.4.1    atom4R_0.3-3     
## [19] stringr_1.5.1     keyring_1.3.2     htmltools_0.5.8.1
## [22] sass_0.4.9        pillar_1.9.0      crayon_1.5.3     
## [25] jquerylib_0.1.4   whisker_0.4.1     tidyr_1.3.1      
## [28] R.utils_2.12.3    cachem_1.1.0      zen4R_0.10       
## [31] tidyselect_1.2.1  zip_2.3.1         digest_0.6.37    
## [34] stringi_1.8.4     dplyr_1.1.4       purrr_1.0.2      
## [37] fastmap_1.2.0     cli_3.6.3         magrittr_2.0.3   
## [40] XML_3.99-0.17     crul_1.5.0        utf8_1.2.4       
## [43] withr_3.0.2       osfr_0.2.9        bit64_4.5.2      
## [46] roxygen2_7.3.2    rmarkdown_2.29    httr_1.4.7       
## [49] bit_4.5.0         qpdf_1.3.4        askpass_1.2.1    
## [52] R.methodsS3_1.8.2 hms_1.1.3         memoise_2.0.1    
## [55] evaluate_1.0.1    rlang_1.1.4       Rcpp_1.0.13-1    
## [58] glue_1.8.0        httpcode_0.3.0    xml2_1.3.6       
## [61] fauxpas_0.5.2     rorcid_0.7.0      vroom_1.6.5      
## [64] jsonlite_1.8.9    plyr_1.8.9        R6_2.5.1         
## [67] fs_1.6.5